WHAT IF Check report

This file was created 2012-04-04 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb2laa.ent

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A; Model number 1

Note: Ramachandran plot

Chain identifier: A; Model number 2

Note: Ramachandran plot

Chain identifier: A; Model number 3

Note: Ramachandran plot

Chain identifier: A; Model number 4

Note: Ramachandran plot

Chain identifier: A; Model number 5

Note: Ramachandran plot

Chain identifier: A; Model number 6

Note: Ramachandran plot

Chain identifier: A; Model number 7

Note: Ramachandran plot

Chain identifier: A; Model number 8

Note: Ramachandran plot

Chain identifier: A; Model number 9

Note: Ramachandran plot

Chain identifier: A; Model number 10

Note: Ramachandran plot

Chain identifier: A; Model number 11

Note: Ramachandran plot

Chain identifier: A; Model number 12

Note: Ramachandran plot

Chain identifier: A; Model number 13

Note: Ramachandran plot

Chain identifier: A; Model number 14

Note: Ramachandran plot

Chain identifier: A; Model number 15

Note: Ramachandran plot

Chain identifier: A; Model number 16

Note: Ramachandran plot

Chain identifier: A; Model number 17

Note: Ramachandran plot

Chain identifier: A; Model number 18

Note: Ramachandran plot

Chain identifier: A; Model number 19

Note: Ramachandran plot

Chain identifier: A; Model number 20

Coordinate problems, unexpected atoms, B-factor and occupancy checks

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   1 GLY   ( 420-)  A    Zero
   2 GLY   ( 421-)  A    Zero
   3 THR   ( 422-)  A    Zero
   4 GLY   ( 423-)  A    Zero
   5 ASN   ( 424-)  A    Zero
   6 LYS   ( 425-)  A    Zero
   7 VAL   ( 426-)  A    Zero
   8 THR   ( 427-)  A    Zero
   9 ILE   ( 428-)  A    Zero
  10 TYR   ( 429-)  A    Zero
  11 TYR   ( 430-)  A    Zero
  12 LYS   ( 431-)  A    Zero
  13 LYS   ( 432-)  A    Zero
  14 GLY   ( 433-)  A    Zero
  15 PHE   ( 434-)  A    Zero
  16 ASN   ( 435-)  A    Zero
  17 SER   ( 436-)  A    Zero
  18 PRO   ( 437-)  A    Zero
  19 TYR   ( 438-)  A    Zero
  20 ILE   ( 439-)  A    Zero
  21 HIS   ( 440-)  A    Zero
  22 TYR   ( 441-)  A    Zero
  23 ARG   ( 442-)  A    Zero
  24 PRO   ( 443-)  A    Zero
  25 ALA   ( 444-)  A    Zero
And so on for a total of 2080 lines.

Nomenclature related problems

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

  39 ASP   ( 458-)  A
  51 ASP   ( 470-)  A
 155 ASP   ( 470-)  A
 259 ASP   ( 470-)  A
 278 ASP   ( 489-)  A
 363 ASP   ( 470-)  A
 455 ASP   ( 458-)  A
 486 ASP   ( 489-)  A
 571 ASP   ( 470-)  A
 663 ASP   ( 458-)  A
 779 ASP   ( 470-)  A
 798 ASP   ( 489-)  A
 896 ASP   ( 483-)  A
 987 ASP   ( 470-)  A 1
1079 ASP   ( 458-)  A 1
1091 ASP   ( 470-)  A 1
1110 ASP   ( 489-)  A 1
1183 ASP   ( 458-)  A 1
1208 ASP   ( 483-)  A 1
1214 ASP   ( 489-)  A 1
1318 ASP   ( 489-)  A 1
1391 ASP   ( 458-)  A 1
1403 ASP   ( 470-)  A 1
1611 ASP   ( 470-)  A 1
1728 ASP   ( 483-)  A 1
1734 ASP   ( 489-)  A 1
1819 ASP   ( 470-)  A 1
1832 ASP   ( 483-)  A 1
1923 ASP   ( 470-)  A 1
1942 ASP   ( 489-)  A 1
2040 ASP   ( 483-)  A 2
2046 ASP   ( 489-)  A 2

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

 353 GLU   ( 460-)  A
 371 GLU   ( 478-)  A
 457 GLU   ( 460-)  A
 561 GLU   ( 460-)  A
 769 GLU   ( 460-)  A
 787 GLU   ( 478-)  A
1099 GLU   ( 478-)  A 1
1185 GLU   ( 460-)  A 1
1601 GLU   ( 460-)  A 1
1705 GLU   ( 460-)  A 1
1723 GLU   ( 478-)  A 1
1913 GLU   ( 460-)  A 1

Geometric checks

Note: Per-model averages for bond-length check

The table below gives the per-model bond-length RMS Z-scores.

Model 1 : 0.557
Model 2 : 0.557
Model 3 : 0.558
Model 4 : 0.557
Model 5 : 0.558
Model 6 : 0.558
Model 7 : 0.558
Model 8 : 0.558
Model 9 : 0.558
Model 10 : 0.556
Model 11 : 0.557
Model 12 : 0.558
Model 13 : 0.557
Model 14 : 0.558
Model 15 : 0.555
Model 16 : 0.556
Model 17 : 0.558
Model 18 : 0.558
Model 19 : 0.557
Model 20 : 0.557

Warning: Directionality in bond lengths

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation.

Since this is not an XRAY structure this effect is hard to explain.

Note: Per-model averages for bond-angle check

The table below gives the per-model bond-angle RMS Z-scores.

Model 1 : 0.996
Model 2 : 0.997
Model 3 : 0.997
Model 4 : 0.996
Model 5 : 0.997
Model 6 : 0.996
Model 7 : 0.997
Model 8 : 0.997
Model 9 : 0.996
Model 10 : 0.995
Model 11 : 0.997
Model 12 : 0.996
Model 13 : 0.996
Model 14 : 0.997
Model 15 : 0.996
Model 16 : 0.997
Model 17 : 0.997
Model 18 : 0.997
Model 19 : 0.997
Model 20 : 0.996

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  39 ASP   ( 458-)  A
  51 ASP   ( 470-)  A
 155 ASP   ( 470-)  A
 259 ASP   ( 470-)  A
 278 ASP   ( 489-)  A
 353 GLU   ( 460-)  A
 363 ASP   ( 470-)  A
 371 GLU   ( 478-)  A
 455 ASP   ( 458-)  A
 457 GLU   ( 460-)  A
 486 ASP   ( 489-)  A
 561 GLU   ( 460-)  A
 571 ASP   ( 470-)  A
 663 ASP   ( 458-)  A
 769 GLU   ( 460-)  A
 779 ASP   ( 470-)  A
 787 GLU   ( 478-)  A
 798 ASP   ( 489-)  A
 896 ASP   ( 483-)  A
 987 ASP   ( 470-)  A 1
1079 ASP   ( 458-)  A 1
1091 ASP   ( 470-)  A 1
1099 GLU   ( 478-)  A 1
1110 ASP   ( 489-)  A 1
1183 ASP   ( 458-)  A 1
1185 GLU   ( 460-)  A 1
1208 ASP   ( 483-)  A 1
1214 ASP   ( 489-)  A 1
1318 ASP   ( 489-)  A 1
1391 ASP   ( 458-)  A 1
1403 ASP   ( 470-)  A 1
1601 GLU   ( 460-)  A 1
1611 ASP   ( 470-)  A 1
1705 GLU   ( 460-)  A 1
1723 GLU   ( 478-)  A 1
1728 ASP   ( 483-)  A 1
1734 ASP   ( 489-)  A 1
1819 ASP   ( 470-)  A 1
1832 ASP   ( 483-)  A 1
1913 GLU   ( 460-)  A 1
1923 ASP   ( 470-)  A 1
1942 ASP   ( 489-)  A 1
2040 ASP   ( 483-)  A 2
2046 ASP   ( 489-)  A 2

Note: Per-model averages for chirality check

The table below gives the per-model improper dihedral RMS Z-scores.

Model 1 : 0.741
Model 2 : 0.741
Model 3 : 0.742
Model 4 : 0.742
Model 5 : 0.743
Model 6 : 0.741
Model 7 : 0.741
Model 8 : 0.740
Model 9 : 0.742
Model 10 : 0.741
Model 11 : 0.741
Model 12 : 0.741
Model 13 : 0.742
Model 14 : 0.742
Model 15 : 0.742
Model 16 : 0.741
Model 17 : 0.742
Model 18 : 0.741
Model 19 : 0.742
Model 20 : 0.741

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.415

Note: Per-model averages for Ramachandran check

The table below gives the per-model Ramachandran Z-scores.

Model 1 : -3.402
Model 2 : -3.696
Model 3 : -3.463
Model 4 : -2.994
Model 5 : -3.466
Model 6 : -3.282
Model 7 : -3.181
Model 8 : -3.668
Model 9 : -3.241
Model 10 : -3.563
Model 11 : -3.177
Model 12 : -3.288
Model 13 : -3.430
Model 14 : -3.466
Model 15 : -3.318
Model 16 : -3.360
Model 17 : -3.833
Model 18 : -3.632
Model 19 : -3.330
Model 20 : -3.505

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

1322 THR   ( 493-)  A 1   -3.6
1114 THR   ( 493-)  A 1   -3.6
1842 THR   ( 493-)  A 1   -3.6
2050 THR   ( 493-)  A 2   -3.6
1426 THR   ( 493-)  A 1   -3.6
1738 THR   ( 493-)  A 1   -3.6
 698 THR   ( 493-)  A    -3.6
 386 THR   ( 493-)  A    -3.6
1218 THR   ( 493-)  A 1   -3.6
 282 THR   ( 493-)  A    -3.5
1946 THR   ( 493-)  A 1   -3.5
1634 THR   ( 493-)  A 1   -3.5
 594 THR   ( 493-)  A    -3.5
 906 THR   ( 493-)  A    -3.5
1530 THR   ( 493-)  A 1   -3.5
 802 THR   ( 493-)  A    -3.5
 178 THR   ( 493-)  A    -3.5
1010 THR   ( 493-)  A 1   -3.5
 490 THR   ( 493-)  A    -3.5
  74 THR   ( 493-)  A    -3.5
1043 THR   ( 422-)  A 1   -3.3
1563 THR   ( 422-)  A 1   -2.8
 120 ASN   ( 435-)  A    -2.7
1963 SER   ( 510-)  A 1   -2.7
 923 SER   ( 510-)  A    -2.7
And so on for a total of 305 lines.

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  16 ASN   ( 435-)  A  Poor phi/psi
  32 ALA   ( 451-)  A  PRO omega poor
  34 GLY   ( 453-)  A  Poor phi/psi
  43 SER   ( 462-)  A  Poor phi/psi
  53 GLY   ( 472-)  A  Poor phi/psi
  54 SER   ( 473-)  A  Poor phi/psi
  66 ASN   ( 485-)  A  Poor phi/psi
  72 ASN   ( 491-)  A  Poor phi/psi
  73 ASN   ( 492-)  A  Poor phi/psi
  74 THR   ( 493-)  A  Poor phi/psi
  75 LYS   ( 494-)  A  Poor phi/psi
  76 ASN   ( 495-)  A  Poor phi/psi
  81 THR   ( 500-)  A  Poor phi/psi
  90 ASN   ( 509-)  A  Poor phi/psi
  91 SER   ( 510-)  A  Poor phi/psi
 120 ASN   ( 435-)  A  Poor phi/psi
 136 ALA   ( 451-)  A  PRO omega poor
 138 GLY   ( 453-)  A  Poor phi/psi
 147 SER   ( 462-)  A  Poor phi/psi
 157 GLY   ( 472-)  A  Poor phi/psi
 158 SER   ( 473-)  A  Poor phi/psi
 170 ASN   ( 485-)  A  Poor phi/psi
 177 ASN   ( 492-)  A  Poor phi/psi
 178 THR   ( 493-)  A  Poor phi/psi
 180 ASN   ( 495-)  A  Poor phi/psi
And so on for a total of 273 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -7.531

Note: Per-model averages for chi-1/chi-2 angle check

The table below gives the per-model chi-1/chi-2 correlation Z-scores.

Model 1 : -8.069
Model 2 : -7.813
Model 3 : -7.448
Model 4 : -7.650
Model 5 : -7.166
Model 6 : -7.607
Model 7 : -7.626
Model 8 : -6.993
Model 9 : -7.434
Model 10 : -7.581
Model 11 : -7.582
Model 12 : -7.421
Model 13 : -7.471
Model 14 : -7.771
Model 15 : -7.956
Model 16 : -6.943
Model 17 : -7.480
Model 18 : -7.651
Model 19 : -7.490
Model 20 : -7.462

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 THR   ( 422-)  A      0
  13 LYS   ( 432-)  A      0
  15 PHE   ( 434-)  A      0
  16 ASN   ( 435-)  A      0
  17 SER   ( 436-)  A      0
  25 ALA   ( 444-)  A      0
  29 TRP   ( 448-)  A      0
  31 ALA   ( 450-)  A      0
  32 ALA   ( 451-)  A      0
  33 PRO   ( 452-)  A      0
  34 GLY   ( 453-)  A      0
  35 VAL   ( 454-)  A      0
  38 GLN   ( 457-)  A      0
  40 ALA   ( 459-)  A      0
  41 GLU   ( 460-)  A      0
  42 ILE   ( 461-)  A      0
  43 SER   ( 462-)  A      0
  45 TYR   ( 464-)  A      0
  52 ILE   ( 471-)  A      0
  54 SER   ( 473-)  A      0
  57 GLN   ( 476-)  A      0
  63 ASN   ( 482-)  A      0
  64 ASP   ( 483-)  A      0
  66 ASN   ( 485-)  A      0
  67 ASN   ( 486-)  A      0
And so on for a total of 1086 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 0.283

Note: Per-model averages for omega angle check

The table below gives the per-model omega angle standard deviations.

Model 1 : 0.054
Model 2 : 0.106
Model 3 : 0.000
Model 4 : 0.134
Model 5 : 0.000
Model 6 : 0.071
Model 7 : 0.059
Model 8 : 0.000
Model 9 : 0.000
Model 10 : 0.000
Model 11 : 0.000
Model 12 : 0.064
Model 13 : 0.000
Model 14 : 0.000
Model 15 : 0.050
Model 16 : 0.000
Model 17 : 0.000
Model 18 : 0.150
Model 19 : 0.000
Model 20 : 0.095

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

1093 GLY   ( 472-)  A 1  3.33   10
1301 GLY   ( 472-)  A 1  3.28   11
1509 GLY   ( 472-)  A 1  3.25   11
 261 GLY   ( 472-)  A   3.24   11
1961 GLY   ( 508-)  A 1  3.01   49
1753 GLY   ( 508-)  A 1  2.81   50
 609 GLY   ( 508-)  A   2.64   51
1129 GLY   ( 508-)  A 1  2.64   50
2065 GLY   ( 508-)  A 2  2.63   50
1337 GLY   ( 508-)  A 1  2.59   47
 713 GLY   ( 508-)  A   2.51   56
 817 GLY   ( 508-)  A   2.50   74
1025 GLY   ( 508-)  A 1  2.50   77
 401 GLY   ( 508-)  A   2.46   76
1233 GLY   ( 508-)  A 1  2.45   64
1441 GLY   ( 508-)  A 1  2.41   62
 193 GLY   ( 508-)  A   2.39   62
1857 GLY   ( 508-)  A 1  2.29   65
 505 GLY   ( 508-)  A   2.26   66
1668 GLY   ( 423-)  A 1  1.84   38
1980 GLY   ( 423-)  A 2  1.67   42
1772 GLY   ( 423-)  A 1  1.65   11
 628 GLY   ( 423-)  A   1.65   10
1538 GLY   ( 501-)  A 1  1.57   10
 914 GLY   ( 501-)  A   1.51   10

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  18 PRO   ( 437-)  A    0.18 LOW
  24 PRO   ( 443-)  A    0.18 LOW
  33 PRO   ( 452-)  A    0.18 LOW
  88 PRO   ( 507-)  A    0.18 LOW
 102 PRO   ( 521-)  A    0.18 LOW
 122 PRO   ( 437-)  A    0.18 LOW
 128 PRO   ( 443-)  A    0.18 LOW
 137 PRO   ( 452-)  A    0.18 LOW
 192 PRO   ( 507-)  A    0.18 LOW
 206 PRO   ( 521-)  A    0.18 LOW
 226 PRO   ( 437-)  A    0.18 LOW
 232 PRO   ( 443-)  A    0.18 LOW
 241 PRO   ( 452-)  A    0.18 LOW
 296 PRO   ( 507-)  A    0.18 LOW
 310 PRO   ( 521-)  A    0.18 LOW
 330 PRO   ( 437-)  A    0.18 LOW
 336 PRO   ( 443-)  A    0.18 LOW
 345 PRO   ( 452-)  A    0.18 LOW
 400 PRO   ( 507-)  A    0.18 LOW
 414 PRO   ( 521-)  A    0.18 LOW
 434 PRO   ( 437-)  A    0.18 LOW
 440 PRO   ( 443-)  A    0.18 LOW
 449 PRO   ( 452-)  A    0.18 LOW
 504 PRO   ( 507-)  A    0.18 LOW
 518 PRO   ( 521-)  A    0.18 LOW
And so on for a total of 100 lines.

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively).

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. However, as this seems to be an NMR structure, this is unlikely to happen in this report.

1269 HIS   ( 440-)  A 1    CD2 <-> 1277 TRP   ( 448-)  A 1    CE3    0.56    2.64
1581 HIS   ( 440-)  A 1    CD2 <-> 1589 TRP   ( 448-)  A 1    CE3    0.55    2.65
1256 THR   ( 427-)  A 1    CG2 <-> 1258 TYR   ( 429-)  A 1    CE1    0.48    2.72
 424 THR   ( 427-)  A      CG2 <->  426 TYR   ( 429-)  A      CE1    0.47    2.73
 320 THR   ( 427-)  A      CG2 <->  322 TYR   ( 429-)  A      CE1    0.47    2.73
 112 THR   ( 427-)  A      CG2 <->  114 TYR   ( 429-)  A      CE1    0.47    2.73
 591 SER   ( 490-)  A      O   <->  594 THR   ( 493-)  A      N      0.47    2.23
1880 THR   ( 427-)  A 1    CG2 <-> 1882 TYR   ( 429-)  A 1    CE1    0.47    2.73
   8 THR   ( 427-)  A      CG2 <->   10 TYR   ( 429-)  A      CE1    0.47    2.73
 653 TRP   ( 448-)  A      CZ2 <->  700 ASN   ( 495-)  A      ND2    0.47    2.63
 957 HIS   ( 440-)  A 1    NE2 <->  965 TRP   ( 448-)  A 1    CE3    0.46    2.64
1672 THR   ( 427-)  A 1    CG2 <-> 1674 TYR   ( 429-)  A 1    CE1    0.46    2.74
1048 THR   ( 427-)  A 1    CG2 <-> 1050 TYR   ( 429-)  A 1    CE1    0.46    2.74
 840 THR   ( 427-)  A      CG2 <->  842 TYR   ( 429-)  A      CE1    0.46    2.74
1360 THR   ( 427-)  A 1    CG2 <-> 1362 TYR   ( 429-)  A 1    CE1    0.46    2.74
1152 THR   ( 427-)  A 1    CG2 <-> 1154 TYR   ( 429-)  A 1    CE1    0.46    2.74
 736 THR   ( 427-)  A      CG2 <->  738 TYR   ( 429-)  A      CE1    0.46    2.74
 632 THR   ( 427-)  A      CG2 <->  634 TYR   ( 429-)  A      CE1    0.46    2.74
 528 THR   ( 427-)  A      CG2 <->  530 TYR   ( 429-)  A      CE1    0.46    2.74
 216 THR   ( 427-)  A      CG2 <->  218 TYR   ( 429-)  A      CE1    0.46    2.74
 944 THR   ( 427-)  A 1    CG2 <->  946 TYR   ( 429-)  A 1    CE1    0.45    2.75
1831 ASN   ( 482-)  A 1    ND2 <-> 1837 TRP   ( 488-)  A 1    CE3    0.45    2.65
1215 SER   ( 490-)  A 1    O   <-> 1218 THR   ( 493-)  A 1    N      0.44    2.26
1943 SER   ( 490-)  A 1    O   <-> 1946 THR   ( 493-)  A 1    N      0.44    2.26
1269 HIS   ( 440-)  A 1    NE2 <-> 1277 TRP   ( 448-)  A 1    CE3    0.44    2.66
And so on for a total of 2052 lines.

Packing, accessibility and threading

Note: Per-model averages for inside/outside residue distributi ...heck




















Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 1

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 2

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 3

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 4

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 5

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 6

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 7

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 8

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 9

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 10

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 11

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 12

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 13

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 14

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 15

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 16

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 17

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 18

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 19

Note: Inside/Outside RMS Z-score plot

Chain identifier: A; Model number 20

Warning: Abnormal packing environment for some residues


Warning: Abnormal packing environment for sequential residues


Note: Quality value plot

Chain identifier: A; Model number 1

Note: Quality value plot

Chain identifier: A; Model number 2

Note: Quality value plot

Chain identifier: A; Model number 3

Note: Quality value plot

Chain identifier: A; Model number 4

Note: Quality value plot

Chain identifier: A; Model number 5

Note: Quality value plot

Chain identifier: A; Model number 6

Note: Quality value plot

Chain identifier: A; Model number 7

Note: Quality value plot

Chain identifier: A; Model number 8

Note: Quality value plot

Chain identifier: A; Model number 9

Note: Quality value plot

Chain identifier: A; Model number 10

Note: Quality value plot

Chain identifier: A; Model number 11

Note: Quality value plot

Chain identifier: A; Model number 12

Note: Quality value plot

Chain identifier: A; Model number 13

Note: Quality value plot

Chain identifier: A; Model number 14

Note: Quality value plot

Chain identifier: A; Model number 15

Note: Quality value plot

Chain identifier: A; Model number 16

Note: Quality value plot

Chain identifier: A; Model number 17

Note: Quality value plot

Chain identifier: A; Model number 18

Note: Quality value plot

Chain identifier: A; Model number 19

Note: Quality value plot

Chain identifier: A; Model number 20

Warning: Low packing Z-score for some residues


Note: Per-model averages for NQA




















Note: Second generation quality Z-score plot

Chain identifier: A; Model number 1

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 2

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 3

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 4

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 5

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 6

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 7

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 8

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 9

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 10

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 11

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 12

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 13

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 14

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 15

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 16

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 17

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 18

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 19

Note: Second generation quality Z-score plot

Chain identifier: A; Model number 20

Water, ion, and hydrogenbond related checks

Error: HIS, ASN, GLN side chain flips


Warning: Buried unsatisfied hydrogen bond donors


Warning: Buried unsatisfied hydrogen bond acceptors


Warning: No crystallisation information

Warning: Possible wrong residue type


Final summary

Note: Summary report for users of a structure